Reader to read file formats supported by itk. More...

#include <mitkItkImageFileReader.h>

Inheritance diagram for mitk::ItkImageFileReader:

Collaboration diagram for mitk::ItkImageFileReader:

Public Types
typedef ItkImageFileReader	Self
typedef FileReader	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
Public Member Functions
virtual const char *	GetClassName () const
virtual void	SetFileName (const char *_arg)
	Specify the file to load.
virtual const char *	GetFileName () const
	Get the specified the file to load.
virtual void	SetFilePrefix (const char *_arg)
	Specify file prefix for the file(s) to load.
virtual const char *	GetFilePrefix () const
	Get the specified file prefix for the file(s) to load.
virtual void	SetFilePattern (const char *_arg)
	Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
virtual const char *	GetFilePattern () const
	Get the specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
Static Public Member Functions
static Pointer	New ()
static bool	CanReadFile (const std::string filename, const std::string filePrefix, const std::string filePattern)
Protected Member Functions
virtual void	GenerateData ()
	A version of GenerateData() specific for image processing filters.
	ItkImageFileReader ()
	~ItkImageFileReader ()
Protected Attributes
std::string	m_FileName
std::string	m_FilePrefix
std::string	m_FilePattern

Detailed Description

Reader to read file formats supported by itk.

Definition at line 30 of file mitkItkImageFileReader.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::ItkImageFileReader::ConstPointer

Definition at line 33 of file mitkItkImageFileReader.h.

typedef itk::SmartPointer<Self> mitk::ItkImageFileReader::Pointer

Definition at line 33 of file mitkItkImageFileReader.h.

typedef ItkImageFileReader mitk::ItkImageFileReader::Self

Definition at line 33 of file mitkItkImageFileReader.h.

typedef FileReader mitk::ItkImageFileReader::Superclass

Definition at line 33 of file mitkItkImageFileReader.h.

Constructor & Destructor Documentation

mitk::ItkImageFileReader::ItkImageFileReader ( ) [protected]

Definition at line 178 of file mitkItkImageFileReader.cpp.

    : m_FileName(""), m_FilePrefix(""), m_FilePattern("")
{
}

mitk::ItkImageFileReader::~ItkImageFileReader ( ) [protected]

Definition at line 183 of file mitkItkImageFileReader.cpp.

{
}

Member Function Documentation

bool mitk::ItkImageFileReader::CanReadFile	(	const std::string	filename,
		const std::string	filePrefix,
		const std::string	filePattern
	)		`[static]`

Definition at line 161 of file mitkItkImageFileReader.cpp.

{
  // First check the extension
  if(  filename == "" )
    return false;

  // check if image is serie
  if( filePattern != "" && filePrefix != "" )
    return false;

  itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO( filename.c_str(), itk::ImageIOFactory::ReadMode );
  if ( imageIO.IsNull() )
    return false;

  return true;
}

void mitk::ItkImageFileReader::GenerateData ( ) [protected, virtual]

A version of GenerateData() specific for image processing filters.

This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also:: ThreadedGenerateData()

Reimplemented from mitk::ImageSource.

Definition at line 38 of file mitkItkImageFileReader.cpp.

References mitk::Geometry3D::GetIndexToWorldTransform(), mitk::ImageSource::GetOutput(), mitk::PixelType::Initialize(), mitk::SlicedGeometry3D::InitializeEvenlySpaced(), m_FileName, mitk::Image::ManageMemory, matrix(), MITK_INFO, mitk::Geometry3D::SetOrigin(), and mitk::SlicedGeometry3D::SetSpacing().

{
  mitk::Image::Pointer image = this->GetOutput();

  const unsigned int MINDIM = 2;
  const unsigned int MAXDIM = 4;

  MITK_INFO << "loading " << m_FileName << " via itk::ImageIOFactory... " << std::endl;

  // Check to see if we can read the file given the name or prefix
  if ( m_FileName == "" )
  {
    itkWarningMacro( << "File Type not supported!" );
    return ;
  }

  itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO( m_FileName.c_str(), itk::ImageIOFactory::ReadMode );
  if ( imageIO.IsNull() )
  {
    itkWarningMacro( << "File Type not supported!" );
    return ;
  }

  // Got to allocate space for the image. Determine the characteristics of
  // the image.
  imageIO->SetFileName( m_FileName.c_str() );
  imageIO->ReadImageInformation();

  unsigned int ndim = imageIO->GetNumberOfDimensions();
  if ( ndim < MINDIM || ndim > MAXDIM )
  {
    itkWarningMacro( << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D." );
    ndim = MAXDIM;
  }

  itk::ImageIORegion ioRegion( ndim );
  itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
  itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();

  unsigned int dimensions[ MAXDIM ];
  dimensions[ 0 ] = 0;
  dimensions[ 1 ] = 0;
  dimensions[ 2 ] = 0;
  dimensions[ 3 ] = 0;

  float spacing[ MAXDIM ];
  spacing[ 0 ] = 1.0f;
  spacing[ 1 ] = 1.0f;
  spacing[ 2 ] = 1.0f;
  spacing[ 3 ] = 1.0f;

  Point3D origin;
  origin.Fill(0);

  unsigned int i;
  for ( i = 0; i < ndim ; ++i )
  {
    ioStart[ i ] = 0;
    ioSize[ i ] = imageIO->GetDimensions( i );
    if(i<MAXDIM)
    {
      dimensions[ i ] = imageIO->GetDimensions( i );
      spacing[ i ] = imageIO->GetSpacing( i );
      if(spacing[ i ] <= 0)
        spacing[ i ] = 1.0f;
    }
    if(i<3)
    {
      origin[ i ] = imageIO->GetOrigin( i );
    }
  }

  ioRegion.SetSize( ioSize );
  ioRegion.SetIndex( ioStart );

  MITK_INFO << "ioRegion: " << ioRegion << std::endl;
  imageIO->SetIORegion( ioRegion );
  void* buffer = new unsigned char[imageIO->GetImageSizeInBytes()];
  imageIO->Read( buffer );
  //mitk::Image::Pointer image = mitk::Image::New();
  if((ndim==4) && (dimensions[3]<=1))
    ndim = 3;
  if((ndim==3) && (dimensions[2]<=1))
    ndim = 2;
  mitk::PixelType pixelType( imageIO->GetComponentTypeInfo(), imageIO->GetNumberOfComponents(), imageIO->GetPixelType() );
  image->Initialize( pixelType, ndim, dimensions );
  image->SetImportChannel( buffer, 0, Image::ManageMemory );

  // access direction of itk::Image and include spacing
  mitk::Matrix3D matrix;
  matrix.SetIdentity();
  unsigned int j, itkDimMax3 = (ndim >= 3? 3 : ndim);
  for ( i=0; i < itkDimMax3; ++i)
    for( j=0; j < itkDimMax3; ++j )
      matrix[i][j] = imageIO->GetDirection(j)[i];

  // re-initialize PlaneGeometry with origin and direction
  PlaneGeometry* planeGeometry = static_cast<PlaneGeometry*>(image->GetSlicedGeometry(0)->GetGeometry2D(0));
  planeGeometry->SetOrigin(origin);
  planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);

  // re-initialize SlicedGeometry3D
  SlicedGeometry3D* slicedGeometry = image->GetSlicedGeometry(0);
  slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
  slicedGeometry->SetSpacing(spacing);

  // re-initialize TimeSlicedGeometry
  image->GetTimeSlicedGeometry()->InitializeEvenlyTimed(slicedGeometry, image->GetDimension(3));

  buffer = NULL;
  MITK_INFO << "number of image components: "<< image->GetPixelType().GetNumberOfComponents() << std::endl;
//  mitk::DataNode::Pointer node = this->GetOutput();
//  node->SetData( image );

  // add level-window property
  //if ( image->GetPixelType().GetNumberOfComponents() == 1 )
  //{
  //  SetDefaultImageProperties( node );
  //} 
  MITK_INFO << "...finished!" << std::endl;
}

virtual const char* mitk::ItkImageFileReader::GetClassName ( ) const [virtual]

virtual const char* mitk::ItkImageFileReader::GetFileName ( ) const [virtual]

Get the specified the file to load.

Either the FileName or FilePrefix plus FilePattern are used to read.

Implements mitk::FileReader.

virtual const char* mitk::ItkImageFileReader::GetFilePattern ( ) const [virtual]

Get the specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

virtual const char* mitk::ItkImageFileReader::GetFilePrefix ( ) const [virtual]

Get the specified file prefix for the file(s) to load.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

static Pointer mitk::ItkImageFileReader::New ( ) [static]

Method for creation through the object factory.

Reimplemented from mitk::ImageSource.

virtual void mitk::ItkImageFileReader::SetFileName ( const char * aFileName ) [virtual]

Specify the file to load.

Either the FileName or FilePrefix plus FilePattern are used to read.

Implements mitk::FileReader.

virtual void mitk::ItkImageFileReader::SetFilePattern ( const char * aFilePattern ) [virtual]

Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

virtual void mitk::ItkImageFileReader::SetFilePrefix ( const char * aFilePrefix ) [virtual]

Specify file prefix for the file(s) to load.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

Member Data Documentation

std::string mitk::ItkImageFileReader::m_FileName [protected]

Definition at line 57 of file mitkItkImageFileReader.h.

Referenced by GenerateData().

std::string mitk::ItkImageFileReader::m_FilePattern [protected]

Definition at line 61 of file mitkItkImageFileReader.h.

std::string mitk::ItkImageFileReader::m_FilePrefix [protected]

Definition at line 59 of file mitkItkImageFileReader.h.

The documentation for this class was generated from the following files:

mitk::ItkImageFileReader Class Reference [IO Classes]

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

mitk::ItkImageFileReader Class Reference
[IO Classes]